I think you're looking at the political leadership, so I'll comment on that.

Empires like the Il-Khanate, Seljuks, or Il-Khanate, or any of the various Turkic groups that propped up in between or after those three, were certainly foreign in nature (either Mongols or Turkmen). After the fall of the Sassanid dynasty to the muslim invasions of the 6-700's, the region was occupied by one foreign dynasty or another until the rise of the Safavids.

Culturally speaking, a lot of things changed in Iran between the Sassanids and the Safavids. That being said, the people remained ultimately Iranian and managed to reassert a native dynasty. So while the political leadership may have been non-Iranian at many times, the "civilization" itself was never really removed.